monocle (version 1.6.2)

plot_genes_positive_cells: Plots the number of cells expressing one or more genes as a barplot

Description

Plots the number of cells expressing one or more genes as a barplot

Usage

plot_genes_positive_cells(cds_subset, grouping = "State", min_expr = 0.1,
  nrow = NULL, ncol = 1, panel_order = NULL, plot_as_fraction = TRUE,
  label_by_short_name = TRUE)

Arguments

cds_subset

CellDataSet for the experiment

grouping

the cell attribute (e.g. the column of pData(cds)) to group cells by on the horizontal axis

min_expr

the minimum (untransformed) expression level to use in plotted the genes.

nrow

the number of rows used when laying out the panels for each gene's expression

ncol

the number of columns used when laying out the panels for each gene's expression

panel_order

the order in which genes should be layed out (left-to-right, top-to-bottom)

plot_as_fraction

whether to show the percent instead of the number of cells expressing each gene

label_by_short_name

label figure panels by gene_short_name (TRUE) or feature id (FALSE)

Value

• a ggplot2 plot object

Examples

data(HSMM)
MYOG_ID1 <- HSMM[row.names(subset(fData(HSMM), gene_short_name %in% c("MYOG", "ID1"))),]
plot_genes_positive_cells(MYOG_ID1, grouping="Media", ncol=2)